sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
4594ff82d3656a4f4f230a9b98905215cec73170f1d42d817306d50dea99faa8 | MATLAB | 2,576 | 117 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
4ec686c3f13faa32059b3c178b04a85c0d41eb9ce81325e1a98376db5fb5f794 | MATLAB | 2,580 | 82 | function info = LoadSBXinfo(inputPath) % input path can be .sbx or .mat
% Make sure we're opening the info .mat file
[inputDir, inputName, inputExt] = fileparts(inputPath);
% Find the name of the info file and load it
if ~isempty(inputDir), inputDir = [inputDir '\']; end
basePath = [inputDir inputName];
infoP... |
4fe012f430041f6df9b30a5b9ecc73f4d113af30e196c30fe0b56936a3a7e5a7 | MATLAB | 2,580 | 115 | % op_takecoils.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% out=op_takecoils(in,index);
%
% DESCRIPTION:
% Extract the rf coil channels with indices corresponding to the 'index' input
% array.
%
% INPUTS:
% in = input data in matlab structure format.
% index = vector indicating the indices of the rf ch... |
69d3ae04d4d387b8e590c7189b6960a21488fb40eb9772ce2d67e5a1741c9864 | MATLAB | 2,581 | 71 | function [PERFORMANCE, NETS, numfeatures] = ...
nnSearchParams(DataRank,DataTestRank,y,yTest)
% Now take the ranked features and test them in multiple neural network
% architectures
numfeatures = 5:5:size(DataRank,2); % number of inputs (features)
u1 = 5:5:15; % number of units in the first hidden... |
6191165203c79420970bd781c62d7807882f2d96d3934ee3f3be73f487c6bda6 | MATLAB | 2,582 | 62 | function t2n_initModelfolders(folder)
% This function initializes a new folder in which all necessary files and
% folders are created to start a new a compartmental model featuring T2N
%
% INPUTS
% folder (optional) path to the folder which should be
% initialized/created.
%
%
% *... |
48588775a08ac8c1dd90d63af62704dbb661b149aeac2826ac7b237d159c8807 | MATLAB | 2,584 | 80 | function result = doinheritance(r, tr)
import zapit.yaml.*;
if ~exist('tr','var')
tr = r;
end
result = recurse(r, 0, {tr});
end
function result = recurse(data, level, addit)
import zapit.yaml.*;
if iscell(data) && ~ismymatrix(data)
result = iter_cell(data, level, addit);
elseif isstruct(data... |
6dba416e06e607066d15210890dbf95275b8311b1865709527ccfba65230c561 | MATLAB | 2,586 | 74 | function [stilloffsets] = refs_align(stillimages, maxoffset)
%takes a sequence of STILLIMAGES (numstils x N x N) and returns a matrix
%containing the relative offsets between these images in X and Y based upon
%the shift which gives the maximal cross correlational considered only over
%a range (MAXOFFSET) of offsets ar... |
9294d03edad410c3af4494c269e407aa47c4a893cc7f2d4cd3df4f7b631afc7b | MATLAB | 2,589 | 86 | % sim_press.m
% Robin Simpson and Jamie Near, 2014.
%
% USAGE:
% out = sim_press(n,sw,Bfield,linewidth,sys,tau1,tau2)
%
% DESCRIPTION:
% This function simulates an ideal PRESS experiment with first echo time
% "tau1" and a second echo time of "tau2". The function calls the function
% 'sim_Hamiltonian.m' whi... |
281b0d705553a4708af0402c1737c5192639aec884a7fa246f46981c85f43be3 | MATLAB | 2,590 | 67 | function [ roiStruct ] = selectOrLoadROIs( basePath, flyInd, stackInd, ...
imagingStruct, uiSelection, varargin )
% selectOrLoadROIs Load existent roiStruct from file or select ROIs (do not
% choose overlapping regions!)
%
% Inputs
% ------
%
% basePath: the path up ... |
875fae55aa5da739f268b897510918077de61a0c66fc4b4e1d3b0d9a983d6886 | MATLAB | 2,592 | 55 | function stimConfigLoaded_Callback(obj,~,~)
% Update the GUI when the model's stim config changes
%
% zapit.gui.main.controller.stimConfigLoaded_Callback
%
% Purpose
% Runs whenever zapit.pointer.stimConfig is (re)assigned -- see buildListeners. This
% makes the GUI react to a stim config be... |
db37adc55c3dc8deeb02a67b1702e726d1554083c56b3dae9886844ff7df2e01 | MATLAB | 2,592 | 121 | % ppc: data splitting with a per-class criterion
%
% [Xtr Ytr Xts Yts indices] = ppc(X,Y,ppc)
%
% This function splits the data in X according to the labels in Y and
% returns train and test data, along with the indices in the original data
% vector.
%
% Inputs: - X: data vector
% - Y: labels vector... |
f1ad01c7c39965372c3435871900fa3c6069511b1c8fd63ea213bb3de0c18c5a | MATLAB | 2,592 | 88 | function df = st_compute(df,stim,params)
numFolds = df(1).numFolds;
for fold = 1 :numFolds
fprintf(1,'[%s]:Compute TC Prediction (fold %d) \n',mfilename,fold);
testSet = df(fold).test_set;
fold_stim = stim(:,:,testSet);
x0 = df(fold).x0';
y0 = df(fold).y0';
sigma = df(fold)... |
8706a1e6525b88f7722346ee4ccd76d27492f67749f6d862e5369b0114f4cbe8 | MATLAB | 2,599 | 73 | %% power curve
clc;clear;close all;
%%
% This code plots power curve
% T-test, vary sample sizes
% effect size
Cohensf2 = 0.15;
% SD for normal distribution that governs the correlations of
% non-covariate-related edges
sigma0 = 1;
FWER_threshold = 0.05;
% Number of repetitions
M_rep = 100;
% Number of per... |
18831d927006d42bceb99a2d2ab504119d835967f5446896eb8368d524af220d | MATLAB | 2,600 | 58 | function [controlValues, sensorValues] = generatePoly3Data(varargin)
% Generate a synthetic "semi-linear" laser power curve for testing
%
% function [controlValues, sensorValues] = generatePoly3Data(varargin)
%
% Purpose
% Produce a synthetic laser calibration curve that follows a third order po... |
efa232abcd2ffdfdbd992e4e3e84bfd621a5842c7a7c775f2a7b88d1c71e5004 | MATLAB | 2,600 | 50 | function P_value = permutation_test_ttest(ctrl_mtx, case_mtx, Wp, CID, Clist, M, func, threshold_GT)
% Conducts a permutation test using the t-test to assess the statistical significance
% of a test statistic derived from control and case matrices compared to a permuted dataset.
% Inputs:
% ct... |
877fecb5701d571d5a464852a715bc997a97d6e1ad46869ef43521cd2aaec129 | MATLAB | 2,603 | 72 | %select_spec.m
%
% callback function used for uicontrol popup menu for choosing to select
% MRSI specs to plot. Plots the closest clicked MRSI spec in spm_image GUI.
% must be used with sim_CSIoverlayMRI and spm_image. See
% https://www.mathworks.com/help/matlab/creating_plots/callback-definition.html
% for more info ... |
de1083d86c563fb8ab76cd28cca41b8822b5daf88071b838db4a9ed129520f8c | MATLAB | 2,603 | 55 | function h=subplot_tight(m,n,p,margins,varargin)
%function subplot_tight(m,n,p,margins,varargin)
%
% Functional purpose: A wrapper function for Matlab function subplot. Adds the ability to define the margins between
% neighbouring subplots. Unfotrtunately Matlab subplot function lacks this functionality, and the ma... |
38f669a31521a34d8f53b0852122e7fe7f5683cb422b1094b6fa726be8951c9e | MATLAB | 2,606 | 96 | function [minShifts, probMat] = estimate_offset(chSeq, refImgs, ...
framesPer30sec, maxShift, doPar, varargin)
%% Preallocate offsets
% need inputSequence, maxDx, maxDy, frameRate, doPar, doPlot, verbose
%% Get supplied info
% Image dimensions
[nFrames, nLines, ~] = size(chSeq);
% Parse optional arguments
[verbose... |
ee21ec90a29bab6d90210cdfdeb356947ab99e49a7557e3447dd3c22bec43122 | MATLAB | 2,607 | 89 | %io_writelcm.m
%Jamie Near, McGill University 2014.
%
% USAGE:
% RF=io_writelcm(in,outfile,te);
%
% DESCRIPTION:
% Takes MRS data in matlab structure format and writes it to a text file
% that can be read by LCModel.
%
% INPUTS:
% in = input data in matlab structure format.
% outfile = Desired filename of ... |
291e7530e00d6f0eb85161bbf52d64b6c669a4ce4eafbd2a89d8fe52e7a98795 | MATLAB | 2,608 | 63 | %% Be here:
% Overview script to create bar plots for all kinds of ROIs.
% Johannes Algermissen, 2020.
%
% We are here: cd /project/3017042.02/Analyses/fMRI_Scripts/Run_ROI/Plot_PEs
% Overview script for running all kinds of
% Set directories:
dirs.root = '/project/3017042.02';
dirs.scripts = fullfile(dirs... |
60d64330a60a7078e6a7393a80b2459a532d754fe0cf3fafa3fbc5fa8ec56d33 | MATLAB | 2,612 | 76 | % Preprocessing unit test
%
% oversample
tol = 10e-10;
N = 99;
X = randn(N,1);
% Get default parameters
param = mv_get_preprocess_param('oversample');
%% if data is already balanced then oversampling should have no effect
clabel = ones(N,1);
clabel(N/3+1:2*N/3) = 2;
clabel(2*N/3+1:end) = 3;
[~, ~, clabel2] = mv_pr... |
8e58093c5fa68f4d680fa19535a1aa3e649d88be7e02388ee379e87a30a67877 | MATLAB | 2,614 | 88 | function make_docs_md(varargin)
%make_docs - Publish the documentation as md files
%
% make_docs_md() publishes all m-files contained in the
% CHIPS_rootdir/doc/m/ directory to markdown files, which are output in
% the CHIPS_rootdir/docs directory.
%
% make_docs_md('outputDir', OUTPUTDIR) ouputs the published d... |
5eb60250a569f7d4e781d399a1b5de53995d5e105fbeaf519825b758e2a20c26 | MATLAB | 2,616 | 92 | function figureS5(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
load(fullfile(dataFolder,'simulations','trend_peak_interactions','parameter_changes.mat'));
f = 0.1:0.1:500;
P3 = zeros(length(f),5,5);
P3(:,:,1) = mean(P2(:,:,1:5),... |
f4f1e3abd6a1bfe47277843297e2f9ef7c6689975a9f63db33bcc39275caca6c | MATLAB | 2,619 | 47 |
load('figure_8_data.mat');
% plot thalamocortical and corticothalamic cross-frequency
% information transfer against estimated largest Lyapunov exponents of
% simulated thalamocortical electrodynamics
figure( 'Position', [ 100 0 350 450]);
hold on;
scatter(simulated_anesthesia_lyap(1:end),symlog(simulated_anesthe... |
74440784299edd94db27fd12ccf3a7d756efdd3401c0f7773e4614e3e18a5c05 | MATLAB | 2,620 | 149 |
clear
close all force
warning on
load('a0_0_bhv2trialStrct.mat');
imSize = [733, 977];
load a7_2_createAvergedNOTMorphedHeatMapsLoad.mat
hmAll2 = hmAll;
NIm = [...
1
3
15
16
21
22
32
33
34
43
46
54
58
61
62];
%%
clf
NImFlip = [...
1,1
2,0
3,0
4,0
6,0
9,0
14,0
15,1
16,0
... |
a3a0bcad7f2d48f9b17bd3ee9a7f0a30f635e9947f0f00195f3f065eda74e0ec | MATLAB | 2,622 | 76 | function betas = taft_preprocess_fit_HRF_block(job, data_ups, i_ons)
% betas = taft_preprocess_fit_HRF_trial(job, data_ups, i_ons)
%
% Take upsampled data of entire block (one long vector), fit HRF amplitude
% for every trial within block with one single design matrix for entire
% block.
%
% INPUTS:
% job =... |
df126efea9b64ee941a4ded92b2d9a9616b9fd9e39b9fed6f274b6c2ec8aa9a4 | MATLAB | 2,623 | 108 |
clear
close all force
%load tirals info
load('a0_0_bhv2trialStrct.mat');
load('a1_1_averagingMorphedHeatmaps')
%{
dataExp.sMuscimol'
+1 {'Co_Left_10_M' }
+2 {'Co_Left_10_S' }
+3 {'Co_Left_5_M' }
+4 {'Co_Right_10_M'}
+5 {'Co_Right_10_S'}
+6 {'Co_Right_5_M' }
+7 {'Co_Right_5_S' }
8 {'ML_Bi... |
44e46fc306cdc733665f40ccf0362ba7cbfc1e059fb306bf8b8970f541e9b7d5 | MATLAB | 2,625 | 64 | function [ref_run, ref_scan] = DetermineReference(expt, Tscan, loco, eligible_runs, minStillDur) % refFrame
% Find the longest epoch of stillness within the set of eligbile runs, and use that period as the reference point for registration
if isempty(eligible_runs), eligible_runs = expt.runs; end
%minStillDur = 30;
... |
799e04c5ad418c182bb44244e36fbe0aa3effb84e00a88a459e8827f484bbed2 | MATLAB | 2,627 | 69 | %% power curve
clc;clear;close all;
%%
% This code plots power curve
% Number subjects
n = 50;
% SD for normal distribution that governs the correlations of
% non-covariate-related edges
sigma0 = 1;
FWER_threshold = 0.05;
% Number of repetitions
M_rep = 100;
% Number of permutation tests in one repetition
... |
aa84662e2b6c67e2a6f8e69c7eb2e62ca44a7594b3c3686d834abaa2513ec1f4 | MATLAB | 2,628 | 98 | % SURF_TREE Surface values for tree segments.
% (trees package)
%
% surf = surf_tree (intree, options)
% ----------------------------------
%
% Returns the surface of all tree segments using the X,Y,Z and D
% coordinates and the adjacency matrix [in um2].
%
% Input
% -----
% - intree ::integer: index of tree in tr... |
0bec4372292ca1e41d171570fe73f7350cb8312463ab5fc7ce3d1bd40e4583b9 | MATLAB | 2,631 | 102 | % TYPEN_TREE Tree node B-C-T info.
% (trees package)
%
% typeN = typeN_tree (intree, options)
% ------------------------------------
%
% Returns the BCT string in a vector. This is just the sum of the columns
% in the adjacency matrix and >2 => 2.
% 0 means terminal
% 1 means continuation
% 2 means branch.
%
% Inpu... |
b5159c86113947ae55e0a9284fae2103ef2703a0c02c99a3ffa6e8347e2a9a45 | MATLAB | 2,633 | 62 | function neuron = t2n_as(x,neuron)
% This function adds all missing definition fields to each neuron structure
% in a neuron cell array by telling T2N to use the same fields as those of
% the xth neuron structure in this array. Alternatively it fills up missing
% definitions in a single t2n structure. Useful if many ... |
c5c0ebfce568ddaa6489c4c0fc6ee8b647d5ea4d1b1cd6be5d932c43b89f8f92 | MATLAB | 2,635 | 76 | %% power curve
clc;clear;close all;
%%
% This code plots power curve
% T-test, vary sample sizes
% Number subjects
n = 50;
% SD for normal distribution that governs the correlations of
% non-covariate-related edges
sigma0 = 1;
FWER_threshold = 0.05;
% Number of repetitions
M_rep = 100;
% Number of permutat... |
89259e7a1a71271dbcdb51b42fe428b23c090e651dd4ce31ec8dd338575db08e | MATLAB | 2,641 | 66 | %% Read TDT Fiber Photometry Data into UnfoldToolbox Format
% This example reads fiber photometry data and converts it to
% (<https://www.unfoldtoolbox.org/index.html unfoldtoolbox.org>) format.
% Artifact removal, detrending, dFF calculation is also included.
%% Housekeeping
close all; clear all; clc;
BLOCK... |
ff2792649d02c22fd45686587893565be3cc147e01a8a8e114c33711ffec13dd | MATLAB | 2,645 | 102 | % CHILD_TREE Attribute add-up child node values all nodes in a tree.
% (trees package)
%
% child = child_tree (intree, v, options)
% ---------------------------------------
%
% Returns a vector with the added up values in v of all child nodes
% excluding itself. This is done for each node in the tree. This is a
% ME... |
1cb646fcbe4308aa502add958d6a969fbf0aff197e357c637fd399a4b40a605c | MATLAB | 2,646 | 104 | % IPAR_TREE Path to root: parent indices.
% (trees package)
%
% ipar = ipar_tree (intree, options, ipart)
% -----------------------------------------
%
% Returns the matrix of indices to the parent of individual nodes following
% the path against the direction of the adjacency matrix tocounter the root of
% the tre... |
7b351941264de3edb9b4f888658253fbce86cad2371359379d39db0a7a3e69c0 | MATLAB | 2,646 | 76 | %%% sweep_2D_plots.m
%%% Omkar N. Athavale, May 2023
%%% Plot results from 1D or 2D parameter sweeps
%%% Run the data load section first, then the section of the figure to plot
%% Data load
data_path = '../data/2DSweep_230429201029';
load(data_path)
if length(sweep_var) == 2
v1 = sweep_var(1);
v2 = sweep_var... |
aad126c0c1043357c35e3c9b593de7e9702dfd976204eaa3c438286147895448 | MATLAB | 2,649 | 53 | function P_value = permutation_test_reg(Wm, X, Wp, CID, Clist, M, threshold_GT, Method)
% This function performs a permutation test to evaluate the significance of
% a statistic derived from regression between a matrix Wm and a vector X,
% against permuted data. It uses a specified threshold to calculate... |
459f345948db0333a569eb183693265e8fa36236414a131699e83b30cb80c515 | MATLAB | 2,650 | 91 | function plot_peak_freq_tf(freqmat1, freqmat2, time_vec, plt,...
structure1, structure2, dataset, freq_vec)
%function plot_peak_freq_tf(freqmat1, freqmat2, time_vec, plt,...
% structure1, structure2, dataset, freq_vec)
%
% This function plots the time course of the power spectrum of two signals
% in a variety of... |
3cda16662bdefb19e177b97637be3264772d1da9499a97364698304beda904bf | MATLAB | 2,652 | 76 | % Preprocessing unit test
%
% undersample
tol = 10e-10;
N = 120;
X = randn(N,1);
% Get default parameters
param = mv_get_preprocess_param('undersample');
%% if data is already balanced then undersampling should have no effect
clabel = ones(N,1);
clabel(N/3+1:2*N/3) = 2;
clabel(2*N/3+1:end) = 3;
[~, ~, clabel2] = m... |
ea9d60d366a5790dc81e0cb79ae0e56aa279c3d4d4d70e2e7508d62e683acbd8 | MATLAB | 2,653 | 113 | function sff = sff_xyzt2strk(sff)
%SFF_XYZT2STRK Summary of this function goes here
% Detailed explanation goes here
sff.stk = xyzt2strk(sff.xyzt,sff.prm);
sff.xyztk = sff.stk.xyzti;
end
function strk = xyzt2strk(xyzt,prm)
% build adjacency matrix
strkKernel = determineStrkKernel(xyzt);
adj = bui... |
db8a1824b39ca745c5b05ef2517ff1e709a1e25d97ec5f2805f0de2c491d4e83 | MATLAB | 2,656 | 66 | function fig = t2n_plotVoltSteps(targetfolder_data,neuron,steps,subtract_hv)
% This function plots one or multiple voltage steps, which had been
% previously simulated and saved with t2n_voltSteps. The exact loaded simulation
% is defined by neuron.experiment.
%
% INPUTS
% targetfolder_data destination of temporar... |
102d1898269393d0e2edbf3f4406d72623ecc065561fd38a6bd85020214442aa | MATLAB | 2,657 | 84 | function settingsDirs = possibleSettingsLocations
% Return all possible user settings locations of the Zapit optostim package
%
% function settingsDirs = zapit.settings.possibleSettingsLocations()
%
% Prurpose
% Return all possible user settings directory locations for the Zapit optostim package... |
cc2512853748b19a8b5776527e156e9b39072ae98e45a29efd4a6dd10f2b5a9a | MATLAB | 2,660 | 92 | function TMS_Waveform()
%% Generate TMS pulse trains and write them in a file to be used in the
% NEURON simulation.
% Receive TMS parameters
% 1: Monophasic, 2: Biphasic
TMS_type = menu('Choose TMS pulse type:','Monophasic','Biphasic');
STEP_type = menu('Choose step time (us) :','5','25 (Default)');
%%
prompt = {'... |
ce8408566381c91962eb8d1ff44164a64b78594792c51cc2a86d86083b0c06eb | MATLAB | 2,661 | 81 | function R = simRcvrSens(Nimg,NrcvrXY,NrcvrZ)
% Create receiver sensitivities with ~1/r^2 dependence and linear phase profile.
% Some random fluctuations are introduced to make slightly more realistic.
% Useful for reconstruction simulations.
%
% R = simRcvrSens(Nimg,NrcvrXY,NrcvrZ)
%
% Inputs:
% Nimg: size of ... |
0493eecfcc093ecb4183f7f15cacbe4896cbcf5cdbb22ec5adbe2ea947afc7be | MATLAB | 2,662 | 95 | function varargout = prfs(val, varargin)
%prfs - Check that the value is a positive, real, finite, scalar number
%
% prfs(val) checks that val is a positive, real, finite, scalar number.
% If it is, nothing else happens; if it is not, the function throws an
% exception from the calling function.
%
% prfs(val, '... |
4ec8c93a82602470fb6e3bcd6342d7e9203bc5f80aa81907dd03e0897ff8b9a4 | MATLAB | 2,663 | 96 | function [ciu,Aall,anull,A,ciall,gam_range] = get_MRCC_mammals(K,sam1,sam2,maxC,r1,r2,tau)
%
% INPUTS:
% K: mammals data -> [N*N*M]
% sam1: samples communities first loop
% sam2: samples communities second loop
% maxC: max num communities
% r1: initial gamma low
%... |
a34b70f6454b5913bef883579311d3650d9d1f7cd95e189663b517f129455e8d | MATLAB | 2,663 | 81 | % Let's load first the trees to be simulated
wttrees = load_tree('../data/mtrs/wt_aligned.mtr');%{sample_tree}; % load sample tree
tgtrees = load_tree('../data/mtrs/tg_aligned.mtr');
wteetrees = load_tree('../data/mtrs/wtee_aligned.mtr');%{sample_tree}; % load sample tree
tgeetrees = load_tree('../data/mtrs/tgee_al... |
11664999c1b186767a3be7058442d455af0f5ff52e8c061d33dd753cd33feb74 | MATLAB | 2,664 | 89 | % Classifier unit test
%
% Classifier: ensemble
rng(42)
tol = 10e-10;
% Random data
X = randn(1000,100);
clabel = randi(2, size(X,1),1);
%% ensemble with 1 learner should be identical to testing the classifier directly [two-class LDA]
cfg = [];
cfg.feedback = 0;
cfg.classifier = 'ensemble';
cfg.hyperpara... |
2c17499df0fa399cd7aa43758cf7670719f043c235ccd5b2ae394a4bdc755b28 | MATLAB | 2,664 | 104 | % Handle a couple of edge cases for tuning curve fitting
% To refit an individual cell, the area and the cell number should be uncommented
clear all; close all;
%area = 'V1'; % max fitted spike rate exceeds measured max by a factor of
%10, better fits acheived penalizing fits where the max fitted rate is more ... |
4045723717261521f213355cfb889b61ce2fb2c2a638695b7dec2dd667dd02fb | MATLAB | 2,664 | 84 | function pac_plot_fun_spec(pacmat, ph_freq_vec, amp_freq_vec, measure, ...
structure1, structure2, dataset, sig1, Fs, sig2)
% function pac_plot_fun_spec(pacmat, ph_freq_vec, amp_freq_vec, measure, ...
% structure1, structure2, dataset, sig1, Fs, sig2)
%
% This function plots a PACgram, with the frequency spectra ... |
5cf90a456035e20c67c341529451ee11af09d4e3caf0e51be1f2d112d77512e6 | MATLAB | 2,664 | 80 | function varargout = logTrialToFile(obj, filePath, stimIndex, laserPower, hardwareTriggered, stimDuration)
% Write information on the current trial to the stimulus log file
%
% function fname = zapit.stimConfig.logTrialToFile(obj, filePath, stimIndex, laserPower, hardwareTriggered, stimDuration)
%
%... |
a05d9342c0e5b58f17d72f0886e1fbd8297361c75e0c546255a209a74f248465 | MATLAB | 2,664 | 69 | % Aggregates grand average waveform (GAW) results over all nodes and
% subjects for activity on a slow time scale (< 0.1 Hz)
%
% USAGE:
% GAW = computeGAWs_fast_timescale_agg(GAWnode_filenames)
%
% INPUTS:
% GAWnode_filenames - cell array that contains filenames for results from
% extract_statevar... |
76d8664c0666cad76fe95d1cb6c05394bc0e133399fa7d18e020f93927fe061b | MATLAB | 2,671 | 105 | % ROOT_TREE Add tiny segment at tree root.
% (trees package)
%
% tree = root_tree (intree, options)
% ----------------------------------
%
% Roots a tree by adding tiny segment in the root.
% This function alters the original morphology!
%
% Input
% -----
% - intree ::integer: index of tree in trees or structured... |
7dfa57217794af133afd2dcebada2cddb6b9204680b93c27d2c7114d42bb5037 | MATLAB | 2,671 | 52 | classdef test_regressor_export < matlab.unittest.TestCase
methods (Test)
function writesPackageCompatibleFiles(testCase)
outDir = tempname;
mkdir(outDir);
cleanup = onCleanup(@() rmdir(outDir, 's'));
result = struct();
result.regressors = reshape(... |
82ec60aee1d5a981a8fbd185907377c6201112584d4f2fe6b5932372d9c1c23a | MATLAB | 2,671 | 62 | function [controlValues, sensorValues] = generateSigmoidData(varargin)
% Generate a synthetic sigmoidal laser power curve for testing
%
% function [controlValues, sensorValues] = generateSigmoidData(varargin)
%
% Purpose
% Produce a synthetic laser calibration curve that follows a logistic sigmo... |
925530f055c1c6ee0d67046771229e62114699946246f839b495c919859e59ec | MATLAB | 2,672 | 81 | function varargout = even(val, varargin)
%even - Check that all elements are even integers
%
% even(val) checks that all elements of val are even integers. If they
% are, nothing else happens; if they are not, the function throws an
% exception from the calling function. Integers stored in non integer
% numer... |
270b4e1f639b96ab1a46c106e94f41eeca7de5ea37bb0036d54b3e011d6fa8ed | MATLAB | 2,674 | 72 | function n = t2n_getref(n,neuron,field)
% This function returns the neuron instance that is referenced in neuron
% instance 'n' at field 'field'. If the neuron instance has own definitions
% at 'field', n itsself is returned. The function t2n_as produces such references.
%
% INPUTS
% n index of the neuro... |
5cdab4d52d8c7e9d412c799ad53f981a89360a0880f9c5460238b0653e4a3503 | MATLAB | 2,674 | 86 | % this is time inside eye boundary, see a0_13_insideFaceTiming2
clear
close all force
warning on
imSize = [733, 977];
imSizeCent = fix([733, 977]/2);
%%
y1 = imSizeCent(1)+(-130:70);
x1 = imSizeCent(2)+(-120:0);
y2 = imSizeCent(1)+(-130:70);
x2 = imSizeCent(2)+(0:120);
y1 = [y1(1),y1(end)];
x1 = [x1(1),x1(end)];
y2 ... |
0b432becbc69d236b6426a1947230a371644156f77ed121afe3bebc814a23167 | MATLAB | 2,675 | 79 | function z = LK_CoactivityZScore_20220615(varargin)
%
% LK_CoactivityZScore_20220615 estimates a coactivity z-score between pairs
% of cells during ripples.
%
% Use as: z = LK_CoactivityZScore_20220615(activityCellA, activityCellB)
% or: z = LK_CoactivityZScore_20220615(N, nA, nB, nAB)
%
% Input version #1:
% a... |
e64a0deba7e11625c0761fa45508bcab8b0809351dc6e8e5920f3a5b270df9bf | MATLAB | 2,676 | 65 | %RunElectodesClassificationMatlabFunc
clear all
matlabImpute = true;
imputeIters=20;
NumTreesVec = [80];
substractMouseMean = true;
%LeaveOut = 'Stimuli';
%LeaveOutVec = {'Stimuli','Session','mouse'};
LeaveOutVec = {'mouse'};
%ElectodesClassificationMatlabFunc(unifyContextClasses ,averageAllBoutsFromSession ,.... |
a1dd758369c1ec9847f83b155164c70878ec74de51aa03af3948ff5dd70568f0 | MATLAB | 2,678 | 88 | % op_getSNR.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [SNR]=op_getSNR(in,NAAppmmin,NAAppmmax,noiseppmmin,noiseppmmax,suppressPlots);
%
% DESCRIPTION:
% Find the SNR of the NAA peak in a spectrum.
%
% INPUTS:
% in = input data in matlab structure format
% NAAppmmin = min of frequncy range ... |
beaba7bc54115c63d197b70bbc8a66321d271b6e9b2689db2de415b8cb708b7b | MATLAB | 2,680 | 65 | %RunElectodesClassificationMatlabFunc
clear all
matlabImpute = true;
imputeIters=20;
NumTreesVec = [80];
substractMouseMean = true;
%LeaveOut = 'Stimuli';
%LeaveOutVec = {'Stimuli','Session','mouse'};
LeaveOutVec = {'mouse'};
%ElectodesClassificationMatlabFunc(unifyContextClasses ,averageAllBoutsFromSession ,.... |
b48893f89f685b6f2960efd226c1309d5a61e6e042fe3acca82051a2c5f8da3c | MATLAB | 2,683 | 109 | % FLIP_TREE Flips a tree around one axis.
% (trees package)
%
% tree = flip_tree (intree, DIM, options)
% ---------------------------------------
%
% Flips tree around dimension DIM.
%
% Input
% -----
% - intree ::integer: index of tree in trees or structured tree
% - DIM ::1, 2 or 3: dimension to be flipped
%... |
1623e043f0d7c3fffef868cc61b5451cc0c3842aa97c7dd4bc4d88409f006b9c | MATLAB | 2,685 | 74 | classdef DataDetectSigsDummy < DataDetectSigs
%DataDetectSigsDummy - Data from dummy signal detection
%
% The DataDetectSigsDummy class is a data class that is designed to
% contain all the basic data output from CalcDetectSignalsDummy.
%
% DataDetectSigsDummy public properties inherited from Data:
% mask ... |
7e7a0a110880a5a82b1879d704228bee5e098f7259e13b7ad6e11d405cdc074c | MATLAB | 2,687 | 63 | function ImgGroupObj = from_files(varargin)
%from_files - Create an ImgGroup object from a list of files
%
% OBJ = ImgGroup.from_files() prompts for all required information and
% creates an ImgGroup object from existing files. The resulting children
% will be of the same type and have the same config.
%
% OBJ... |
7008cde6f9668f2a7d18fdc57338032439b9ea77cf63ef9450b8cc1f77cb94c5 | MATLAB | 2,688 | 100 | function respPhase = calculateRespPhase(pulset, time, doHilbert)
% adapted from TAPAS
verbose.level = 2;
resp_max = inf;
overshoot = find(abs(pulset) > resp_max);
pulset(overshoot) = resp_max;
rsampint = time(2) - time(1);
% Compute normalized signal and the sign of the derivative
% pulset = tapas_physio_filter_r... |
bce1823b810eb3c561db26e1cf4909f42cbc9f440251e5df8b110347b3d70f93 | MATLAB | 2,688 | 67 | function x = spatialPattern(DIM,BETA),
% function x = spatialPattern(DIM, BETA),
%
% This function generates 1/f spatial noise, with a normal error
% distribution (the grid must be at least 10x10 for the errors to be normal).
% 1/f noise is scale invariant, there is no spatial scale for which the
% variance pl... |
f6c72876e50d5376cfd8b446cb53444469ff5ebd55fdbbeeb9a0b03a5c051662 | MATLAB | 2,691 | 73 | function check_optList(self)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either version 3 of the License, or
%... |
6756d3aea3f8ffbdd8b63b67ed38158bf73945e22b7098b75698e89ed9b188ac | MATLAB | 2,692 | 88 | % op_blockAvg.m
% Jamie Near, Sunnybrook Research Institute 2024.
%
% USAGE:
% out=op_blockAvg(in,N);
%
% DESCRIPTION:
% Compress a dataset along the averages dimension by combining the averages
% into blocks of N averages. The N averages in each block are then averaged,
% leaving a new dataset with Navg/N transien... |
a49917ec121409ed5bd02116829ea20830210dd6271c037c18f65158c517dbe7 | MATLAB | 2,695 | 99 | %% whiteness
%
% Durbin-Watson test for whiteness (no serial correlation) of VAR residuals
%
% <matlab:open('whiteness.m') code>
%
%% Syntax
%
% [dw,pval] = whiteness(X,E)
%
%% Arguments
%
% See also <mvgchelp.html#4 Common variable names and data structures>.
%
% _input_
%
% X multi-tr... |
bec762af1023497c4dc13e1f3e78d0073211d26dc99ba4cc9b67b3319a1b61e7 | MATLAB | 2,695 | 81 | function aperiodic_sensitivity(iChunk)
% baseFolder = 'E:\Research_Projects\004_Propofol\data\simulations\raw\aperiodic_interactions';
baseFolder = '/lustre04/scratch/nbrake/data/simulations/parameter_sensitivity_analysis_2';
addpath('/lustre04/scratch/nbrake/code/simulation_code');
load(fullfile(baseFolder,'paramete... |
5893d54bc91394ebeddceb41e5ca359040f69d4a1a6dcac9e390dec3ac419bb9 | MATLAB | 2,698 | 69 | function spm_TFCE
% TFCE Toolbox wrapper to call TFCE functions
% ______________________________________________________________________
%
% Christian Gaser
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% ____________________________... |
80c1412f2fefb259ae37412581b5ebde298181ee6a446c9537644c978f0f769d | MATLAB | 2,704 | 93 | function [loglik] = EEGfMRIPav_cbm_mod06(parameters,subj)
% Standard Q-learning model with delta learning rule and with Go bias,
% Pavlovian response bias, and separate learning rate for salient Gos
% (action priming model).
% ----------------------------------------------------------------------- %
%% Retrieve param... |
18ba55b508356a90573759af07dd5f37d80dc4e0a0fe4608d5b8f90aa6450952 | MATLAB | 2,709 | 79 | function masksOut = choose_masks(self, imgTypes)
%choose_masks - Protected class method to choose multiple masks
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as ... |
32c612889cd14da39fee884694078248422a564ec2af4680767c926b3095237c | MATLAB | 2,711 | 95 |
clear
clc
file = '/home/.../.../'; % Load file containing the time series for each participant
mut = -1;
group = 'test';
studygroup = 'all';
ylab = 'age';
[id,y,study,fd,mutation] = load_data(file,mut,group,studygroup,ylab);
if strcmp(group,'test')
load TrainInfo_extra_new.mat
end
disp('selecting links ...')
i... |
39a3679cfa6e2bf50e85790be508bf717f637dc901a2a9437b47eceae367c898 | MATLAB | 2,711 | 98 | % Classifier unit test
%
% Classifier: svm
rng(42) %% do not change - might affect the results
tol = 10e-10;
mf = mfilename;
%% check classifier on multi-class spiral data: linear classifier should near chance, RBF kernel should be near 100%
% Create spiral data
N = 500;
nrevolutions = 2; % how often each cl... |
66bfc9eb9d1b77f1e076f233304fcb78c65beb5af02fa66d7adddfaa9467e464 | MATLAB | 2,712 | 94 | % BIN_TREE Binning nodes in a tree.
% (trees package)
%
% [bi, bins, bh] = bin_tree (intree, v, bins, options)
% ----------------------------------------------------
%
% Subdivides the nodes into bins according to a vector v. This is simply
% the histogram and can be applied for example on x-values, euclidean
% dist... |
9bf9c6362515585e5f9bd7182a541bc651b1cc72883641e15fd3bf84f066dca6 | MATLAB | 2,713 | 96 | %% ICA for fMRI and QSM
%
% Independent component analysis used to see if we can separate breathing /
% cardiac
% fMRI presents the possibility of saving phase data, which can be used for
% QSM or as input to other phase-sensitive MR imaging pipelines
% 10 Aug 2022
% Editors (alphabetical order):
% Alexander Jaffray... |
9e8c3b84711535f969f669a934cc8812b8b098a187a7d7cdd6faf4bd7fdb651a | MATLAB | 2,714 | 87 | function subclasses = find_subclasses(superclass, varargin)
%find_subclasses - Helper function to find subclasses
%
% This function is not intended to be called directly.
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
... |
d1807bbf622557ca3e929ac24e318fd0ab392be48d70b20de1e1f03249259d33 | MATLAB | 2,717 | 71 | classdef Test_CalcFindROIsFLIKA_params < matlab.unittest.TestCase
%Test_CalcFindROIsFLIKA Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
properties (TestParameter)
classCalc_FRF = utils.find_subc... |
e3f27b583e76d5038940f66b2edef5c86778606fd7b9a55247fa5f3ae9dd4228 | MATLAB | 2,717 | 68 | function [imp,freq] = t2n_resonance(neuron,tree,amp,holding_voltage,doerrorbar)
% Perform a resonance test (impedance measurement using oscillating current
% injections) on each cell and plot the result.
%
% INPUTS
% neuron t2n neuron structure with already defined mechanisms
% tree tree cell ar... |
924519bb48076c4ab457c5766650126965b7069bc4c0101198e338373c579c49 | MATLAB | 2,719 | 78 | % detecting the FWHM of a sigle beads
% last modified 2022-05-25
function fullwidth = find_FWHM(new_img)
%---------------------------find the FWHM-------------------------------
%find the center of the intensity plot
% BW = new_img > 0.1;
% CH = bwconvhull(BW);
% imshow(CH);
% hhh = regionprops(CH,'Centroid')... |
25b1783dfbe6538cab169d92cccee9eebd71c6d4504c445a0713c0fe427c1207 | MATLAB | 2,720 | 87 | clear;clc;
close all
load([pwd,'\temporary data\Sub_score.mat']);
Sub_score;
% 30 subject *2 condition *60 frequency*3 score
load([pwd,'\temporary data\fbcca_stime.mat']);
ac_stime;
% 30 subject *2 condition *3 frequency_band *50 data_length
subs=30;
condition=2;
freq_band=3;
frequency=[2 3 4 5 ;12 13 14... |
b3b3ee20020f294b3cc2b4246ebd844dc3781779de6b468faa59fdedf9d30600 | MATLAB | 2,720 | 79 | % the pattern separation toolbox: analyse spike train ensembles
% Copyright (C) 2022 Alexander D Bird
function [output_spiketimes] = spike_thinner_spatiotemporal(input_spiketimes,n_rep,filt_len)
%SPIKE_THINNER_SPATIOTEMPORAL Removes spikes from input trains if they are within
%'filt_len' of any other spike in th... |
7c97c44b40adad14f0c00784098b7017f66006439ce895ef5b0ae1b0b95900a3 | MATLAB | 2,721 | 85 | % SCALEBAR Add a scalebar to an axis.
% (scheme package)
%
% HP = scalebar (unit, pos)
% -------------------------
%
% Adds a scalebar to the axis.
%
% Input
% -----
% - unit ::string: {DEFAULT: micrometer, '\mum'}
% - pos ::string: position {DEFAULT: southwest '-sw'}
% '-sw' : southwest
% '-se' : ... |
2ade02186dfba5cae53601a6faa534fee809a0f25016c980502b0541396fd31f | MATLAB | 2,727 | 87 | function gain = find_gain(chSeq, streak, verbose)
%find_gain - Calculate gain of the optical system
%
% [offsets, refImgs] = find_gain(CHSEQ, STREAK, VERBOSE) takes a movie
% CHSEQ and calculates the GAIN of the optical systemon which the movie
% was recorded by looking at the relationship between the standard
%... |
8ffd4c830663cd65aade1ae45b15955f6920ad4042e35e675168bc4cc352f4f6 | MATLAB | 2,731 | 103 | function dataInterp = interp_masked(self, dataRaw)
%interp_masked - Linearly interpolates data points that have been masked
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public ... |
d4be2cb355798df2066b22254dc5d36ccc72dda8a7bb80e540d2c8617a68096e | MATLAB | 2,732 | 76 | %% Define all relevant parameters and known number of tiles per round
% This is the CA1 complete hippocampus acquired on July 9th-July 14th
% Numbers are from metadata and examining the raw data folders
numTiles = 170;
numRows= 10;
imgSizeXY = [2048, 2048];
imgResXY = .1625; % in um, Taken from the .ims properties re... |
7edbd8bf186e47b00042fe388ace8a84f66743dd75d73c97d3abcb49d7e53182 | MATLAB | 2,733 | 86 | inputname='Gi17547';
timepoint='wk7';
%detect stops(no=0, yes=1)
stopdetect=1;
inputname2=strcat(inputname, '_stimtb.mat');
load(inputname2)
%time resolution for z-score analysis (+/- in sec)
timeres=1
%extract value for control period
d=0;
for c=1:length(LocoSynth);
if LocoSynth(c).time==timepoint;
... |
f2a5df12c782db11c9e506e1866407b7ea1fbb28a750546bd84659fae10c4166 | MATLAB | 2,733 | 87 | function varargout = plot_clsfy(self, hAxes, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation, either vers... |
ffff2663bb63f64d88d381e29b4710f3e9a61c41ac4687ccf160782634b26455 | MATLAB | 2,733 | 75 | function varargout = num_dims(val, nDimIn, varargin)
%num_dims - Check that the variable has the assumed dimensionality
%
% num_dims(val, nDimIn) checks that val has number of dimensions
% specified with nDimIn. If it has, nothing else happens; if it has not,
% the function throws an exception from the calling fu... |
74ff68c23c4fc61377f6b9831d93929c5ad35f0fd0c6fbe3649226f5c933b2f0 | MATLAB | 2,739 | 93 | function children = create_children(self, varargin)
%create_children - Protected class method to create children to add
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public Lice... |
ce4739f4e274ede161a21ac6fb6e8f3de1dd94ebf54e4a67af04a99f8ccac28b | MATLAB | 2,740 | 95 | function [dataOut, varargout] = check_data(self, dataIn, varargin)
%check_data - Check the data and do some other things here for convenience
%
% YY = check_data(OBJ, XX)
%
% MM = check_data(OBJ, XX, DOMEAN)
%
% MM = check_data(OBJ, XX, DOMEAN, DATANAME)
%
% [YY, SEM] = check_data(OBJ, ...)
% Copyright (C) 2... |
22306e373b87be679fff03e9e98a9c8cfbe880daf35a9dbccd1f12b1ff42ad46 | MATLAB | 2,741 | 88 | outname='Gi17547';
outname2=strcat(outname, '_stimtb.mat');
%%last update october 21, 2020
nbpulse=1;
%check the directory, count nb of file
datalist=dir;
nbfile=length(datalist);
nbelem=0;
LocoSynth=[];
%read directory. How many file do we have? create a database.
for a=1:nbfile
if datalist(a).isdir... |
fab2b64d934b970872307d473d2269902f73bea9cac7127f82e4785e961522fc | MATLAB | 2,742 | 84 | function dirs = slice_display_set_dirs(dirs)
% dirs = slice_display_set_dirs(dirs)
%
% Initialize directories, add paths to necessary toolboxes.
% All diretories have defaults (none necessary).
%
% INPUT:
%
% dirs = structure with options (optional settings).
%
% OPTIONAL INPUTS:
% .root = ... |
45bbf0d87af99d31a11b2a8a200e7714414f747062752656a63628cca10d6256 | MATLAB | 2,743 | 71 | function [probMat, subCoords] = fillProbMat( iFrame, ...
chSeq, refImg, maxDy, maxDx, Ny, Nx, numLines)
%fillErrMat - helper function conforming to parfor
% This function calculates absolute error of all possible considered ...
%vertical and horizontal shifts
totLines = (numLines - 2*maxDy);
subCoords = zeros(to... |
8ea876b398d354d37605a050dccdaa2f8f5a4d272005ab8dd537163fdc89f91a | MATLAB | 2,744 | 103 | function varargout = plotStimuli(stim)
% Plot stimulus locations associated with a stim config file
%
% function zapit.utils.plotStimuli(stim)
%
% Purpose
% Plot stimulus conditions as numbered points on a top-down
% atlas view.
%
% Inputs
% stim - Either: 1) Relative or absolu... |
5b49fdd5f811923f8d271b0f7e522b9bf7ba129d87e572804d95379c70eaf246 | MATLAB | 2,746 | 115 | function A = adjacency(DATA, TYPE, PARAM, DISTANCEFUNCTION);
% Compute the adjacency graph of the data set DATA
%
% A = adjacency(DATA, TYPE, PARAM, DISTANCEFUNCTION);
%
% DATA - NxK matrix. Data points are rows.
% TYPE - string 'nn' or string 'epsballs'.
% PARAM - integer if TYPE='nn', real number if TYPE='epsballs... |
687975d2acc09d1954ccdc2ed95c535fb553843331b229cf490cdbd11ef44c51 | MATLAB | 2,747 | 120 | %
clear
close all force
warning on
imSize = [733, 977];
pix2deg = 34.910;
imSizeCent = fix([733, 977]/2);
y1 = imSizeCent(1)+(-130:70);
x1 = imSizeCent(2)+(-120:0);
y2 = imSizeCent(1)+(-130:70);
x2 = imSizeCent(2)+(0:120);
y1 = imSizeCent(1)+(-70:70);
x1 = imSizeCent(2)+(-120:0);
y2 = imSizeCent(1)+(-70:70);
x2 = i... |
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